Pathway Enrichment Analysis


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Current default selection is Model organism, the Ensembl ID background gene file is used on the platform. Please ensure that the Ensembl ID is used for the target genes file in the previous step
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Pathway Enrichment Analysis使用教程

Pathway enrichment analysis tool to use and interpret detailed tutorial

KEGG pathway enrichment analysis provides not only pathway functional annotations of given gene set, but also pathway enrichment analysis. First, Gene numbers of each pathway in a given gene set is calculated. Then significantly enriched pathways in the given gene set comparing to the genome background are defined by hypergeometric test. The calculating formula of P-value is:
Here N is the number of all genes with KEGG pathway annotation; n is the gene number of given genes set in N; M is the number of all genes that are annotated to the certain pathway; m is the gene number in the given gene set that are annotated to the certain pathways. The calculated p-value is gone through FDR Correction, taking FDR ≤ 0.05 as a threshold. Pathways meeting this condition are defined as significantly enriched pathways in the given genes set.


Scope of application:

The gene sets of 18 common species can be enriched and analyzed, including bovine, zebrafish, human, macaque, mouse, rat, pig, elegans, drosophila, Arabidopsis, rice, tomato, wheat, corn, yeast, goat, chicken and indica rice, and 2 genomic versions are provided.

The background genes of the species can also be prepared by themselves for enrichment analysis.



①File format: a tab delimited text file. If your data is not TAB delimited, you can use Excel to convert it.

②Gene set: genes need enrichment analysis. Gene IDs must be separated by new lines and included in the background set. Notice that the file contains only true Gend ids, please check it on the example file.

③Background set: The gene list of background set, usually it's all genes of a genome. The first column is gene id, the second column is gene annotation id. There are three kinds of ID type available: keggid, ncibi-geneid, KO id.

④Gene expression fold change file: the first column is gene names, and the second column is log2 Fold Change value.




①For background set, There are three kinds of ID type available: keggid, ncibi-geneid, KO id

②Species taxonomy: subclass related to your samples such as animal is suggested, but not “all”

③Optional Parameters: add expression fold change of given gene set, and this information will be displayed in KEGG pathway maps.



①out.path.xls:table of enrichment analysis result,content is the same to out.html,including A level classification,B level classification,pathway name, gene number, background gene number, p vaule, Q value,pathway ID,gene id.

②out_map:kegg pathway maps of given genes set.

③out.path.png,out.path.svg:B level classification of pathways in result.

④out.html:analysis result as html format

Example file: given genes set file    background genes set file    fold change file

Representative output result::

Figure1: the page layout of out.html 生物云平台

Figure2: kegg map of out_map 生物云平台

Figure3:pathway classification of out.path.png 生物云平台